Previous nanoparticle aggregate synthesis methods are limited by the variation in aggregate size leading to variation in aggregate morphology. Uncontrolled morphology may lead to inconsistent and irregular behaviors in vivo. Further, such methods result in free reactive groups present in the aggregates, leading to aggregate formation issues and undesired complexation. Accordingly, there is a need in the art for methods of synthesizing nanoparticle aggregates having in-vivo and ex-vivo applications that are formed with stable morphology. Provided herein are solutions to these and other problems in the art.